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<title>MolTK C++ API: moltk::Aligner::Position Class Reference</title>

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      <li class="navelem"><a class="el" href="classmoltk_1_1Aligner_1_1Position.html">Position</a>      </li>
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<div class="title">moltk::Aligner::Position Class Reference</div>  </div>
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<!-- doxytag: class="moltk::Aligner::Position" -->
<p><a class="el" href="classmoltk_1_1Aligner_1_1Position.html" title="Aligner::Position represents a special biosequence residue that knows how to score itself during alig...">Aligner::Position</a> represents a special biosequence residue that knows how to score itself during alignment.  
 <a href="classmoltk_1_1Aligner_1_1Position.html#details">More...</a></p>

<p><code>#include &lt;<a class="el" href="Aligner_8h_source.html">Aligner.h</a>&gt;</code></p>
<div class="dynheader">
Inheritance diagram for moltk::Aligner::Position:</div>
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<div class="center"><img src="classmoltk_1_1Aligner_1_1Position__inherit__graph.png" border="0" usemap="#moltk_1_1Aligner_1_1Position_inherit__map" alt="Inheritance graph"/></div>
<map name="moltk_1_1Aligner_1_1Position_inherit__map" id="moltk_1_1Aligner_1_1Position_inherit__map">
<area shape="rect" id="node3" href="classmoltk_1_1MatrixScorer_1_1Position.html" title="moltk::MatrixScorer::Position" alt="" coords="5,80,195,107"/></map>
<center><span class="legend">[<a href="graph_legend.html">legend</a>]</span></center></div>

<p><a href="classmoltk_1_1Aligner_1_1Position-members.html">List of all members.</a></p>
<table class="memberdecls">
<tr><td colspan="2"><h2><a name="pub-methods"></a>
Public Member Functions</h2></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">virtual <a class="el" href="classmoltk_1_1Aligner_1_1Position.html">Position</a> *&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Aligner_1_1Position.html#a34f4a85b4fd078f833f1c091fd629b2c">clone</a> () const =0</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">virtual&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Aligner_1_1Position.html#a71e3fa5525ce82fc0a501d7ae2ce5803">~Position</a> ()</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">virtual <a class="el" href="namespacemoltk_1_1units.html#ae48aa197908105b66ab2f3649669ff46">moltk::units::Information</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Aligner_1_1Position.html#abee26ee88b3c4b037a19c4f1dff749a4">score</a> (const <a class="el" href="classmoltk_1_1Aligner_1_1Position.html">Position</a> &amp;rhs) const =0</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">virtual char&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Aligner_1_1Position.html#adeb85b03da1c7a2101ca10548acf8e34">getOneLetterCode</a> () const =0</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">virtual <a class="el" href="namespacemoltk_1_1units.html#ae48aa197908105b66ab2f3649669ff46">moltk::units::Information</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Aligner_1_1Position.html#aed5476e1cfb4623e7bb65a713141eb67">gapOpenPenalty</a> () const =0</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">virtual <a class="el" href="namespacemoltk_1_1units.html#ae48aa197908105b66ab2f3649669ff46">moltk::units::Information</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Aligner_1_1Position.html#aa896a3102ef9d955b5a43b431f98a712">gapExtensionPenalty</a> () const =0</td></tr>
</table>
<hr/><a name="details" id="details"></a><h2>Detailed Description</h2>
<div class="textblock"><p><a class="el" href="classmoltk_1_1Aligner_1_1Position.html" title="Aligner::Position represents a special biosequence residue that knows how to score itself during alig...">Aligner::Position</a> represents a special biosequence residue that knows how to score itself during alignment. </p>
</div><hr/><h2>Constructor &amp; Destructor Documentation</h2>
<a class="anchor" id="a71e3fa5525ce82fc0a501d7ae2ce5803"></a><!-- doxytag: member="moltk::Aligner::Position::~Position" ref="a71e3fa5525ce82fc0a501d7ae2ce5803" args="()" -->
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          <td class="memname">virtual moltk::Aligner::Position::~Position </td>
          <td>(</td>
          <td class="paramname"></td><td>)</td>
          <td><code> [inline, virtual]</code></td>
        </tr>
      </table>
</div>
<div class="memdoc">

</div>
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<hr/><h2>Member Function Documentation</h2>
<a class="anchor" id="a34f4a85b4fd078f833f1c091fd629b2c"></a><!-- doxytag: member="moltk::Aligner::Position::clone" ref="a34f4a85b4fd078f833f1c091fd629b2c" args="() const =0" -->
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          <td class="memname">virtual <a class="el" href="classmoltk_1_1Aligner_1_1Position.html">Position</a>* moltk::Aligner::Position::clone </td>
          <td>(</td>
          <td class="paramname"></td><td>)</td>
          <td> const<code> [pure virtual]</code></td>
        </tr>
      </table>
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<div class="memdoc">

<p>Implemented in <a class="el" href="classmoltk_1_1MatrixScorer_1_1Position.html#ab0852e36f23a3640a814d2a0639c6d73">moltk::MatrixScorer::Position</a>.</p>

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<a class="anchor" id="aa896a3102ef9d955b5a43b431f98a712"></a><!-- doxytag: member="moltk::Aligner::Position::gapExtensionPenalty" ref="aa896a3102ef9d955b5a43b431f98a712" args="() const =0" -->
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        <tr>
          <td class="memname">virtual <a class="el" href="namespacemoltk_1_1units.html#ae48aa197908105b66ab2f3649669ff46">moltk::units::Information</a> moltk::Aligner::Position::gapExtensionPenalty </td>
          <td>(</td>
          <td class="paramname"></td><td>)</td>
          <td> const<code> [pure virtual]</code></td>
        </tr>
      </table>
</div>
<div class="memdoc">

<p>Implemented in <a class="el" href="classmoltk_1_1MatrixScorer_1_1Position.html#ac717cf77b2048e497823460b617878eb">moltk::MatrixScorer::Position</a>.</p>

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<a class="anchor" id="aed5476e1cfb4623e7bb65a713141eb67"></a><!-- doxytag: member="moltk::Aligner::Position::gapOpenPenalty" ref="aed5476e1cfb4623e7bb65a713141eb67" args="() const =0" -->
<div class="memitem">
<div class="memproto">
      <table class="memname">
        <tr>
          <td class="memname">virtual <a class="el" href="namespacemoltk_1_1units.html#ae48aa197908105b66ab2f3649669ff46">moltk::units::Information</a> moltk::Aligner::Position::gapOpenPenalty </td>
          <td>(</td>
          <td class="paramname"></td><td>)</td>
          <td> const<code> [pure virtual]</code></td>
        </tr>
      </table>
</div>
<div class="memdoc">

<p>Implemented in <a class="el" href="classmoltk_1_1MatrixScorer_1_1Position.html#a0ddfa7b4cfc344f57bafada41b192b0d">moltk::MatrixScorer::Position</a>.</p>

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<a class="anchor" id="adeb85b03da1c7a2101ca10548acf8e34"></a><!-- doxytag: member="moltk::Aligner::Position::getOneLetterCode" ref="adeb85b03da1c7a2101ca10548acf8e34" args="() const =0" -->
<div class="memitem">
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      <table class="memname">
        <tr>
          <td class="memname">virtual char moltk::Aligner::Position::getOneLetterCode </td>
          <td>(</td>
          <td class="paramname"></td><td>)</td>
          <td> const<code> [pure virtual]</code></td>
        </tr>
      </table>
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<div class="memdoc">

<p>Implemented in <a class="el" href="classmoltk_1_1MatrixScorer_1_1Position.html#add68c5933ad9672aa96d34a3c86b3b02">moltk::MatrixScorer::Position</a>.</p>

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<a class="anchor" id="abee26ee88b3c4b037a19c4f1dff749a4"></a><!-- doxytag: member="moltk::Aligner::Position::score" ref="abee26ee88b3c4b037a19c4f1dff749a4" args="(const Position &amp;rhs) const =0" -->
<div class="memitem">
<div class="memproto">
      <table class="memname">
        <tr>
          <td class="memname">virtual <a class="el" href="namespacemoltk_1_1units.html#ae48aa197908105b66ab2f3649669ff46">moltk::units::Information</a> moltk::Aligner::Position::score </td>
          <td>(</td>
          <td class="paramtype">const <a class="el" href="classmoltk_1_1Aligner_1_1Position.html">Position</a> &amp;&#160;</td>
          <td class="paramname"><em>rhs</em></td><td>)</td>
          <td> const<code> [pure virtual]</code></td>
        </tr>
      </table>
</div>
<div class="memdoc">

<p>Implemented in <a class="el" href="classmoltk_1_1MatrixScorer_1_1Position.html#acd79aecf16ed94660d810af613a35c9c">moltk::MatrixScorer::Position</a>.</p>

</div>
</div>
<hr/>The documentation for this class was generated from the following file:<ul>
<li>C:/Users/cmbruns/svn/moltk/c++/include/moltk/<a class="el" href="Aligner_8h_source.html">Aligner.h</a></li>
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